.beadsRRBeer            Function to run the beads-only round robin
                        using BEER
.beadsRREdgeR           Function to run the beads-only round robin
                        using edgeR
.brewSamples            Run BEER for all samples
.checkCounts            Function to check that the counts matrix only
                        contains integers
.checkOverwrite         Function to check whether an assay will be
                        overwritten
.edgeRBeads             Estimate edgeR dispersion parameters from the
                        beads-only data using qCML
.edgeRBeadsQLF          Estimate edgeR dispersion parameters from the
                        beads-only samples using Cox-Reid profile
                        adjusted likelihood method for estimating
                        dispersions.
.getABEdgeR             Derive beta shape parameters using edgeR
                        dispersion estimates
.getABMLE               Wrapper function to derive MLE estimates of a,
                        b from beads-only samples
.getABMLEProp           Helper function to derive MLE estimates of a, b
                        from a vector of proportions
.getABMOM               Wrapper function to derive MOM estimates of a,
                        b from beads-only samples
.getABMOMProp           Helper function to derive MOM estimates of a, b
                        from a vector of proportions
.guessEnrichedEdgeR     Guess super-enriched peptides based on edgeR
                        fold-change estimates
.guessEnrichedMLE       Guess enriched peptides based on MLE estimates
                        of the true fold-change
.tidyAssayNames         Clean-up specified assay names
.tidyInputsJAGS         Clean inputs for JAGS parameters
.tidyInputsPrior        Clean up inputs for prior estimation
.tidyInputsSE           Clean up inputs for identifying super-enriched
                        peptides
beadsRR                 Beads-only round robin
brew                    Bayesian Enrichment Estimation in R (BEER)
brewOne                 Run BEER for one sample
edgeROne                Run edgeR for one sample against all the
                        beads-only samples.
edgeROneQLF             Run edgeR for one sample against all the
                        beads-only samples using edgeR's QLF Test for
                        differential expression.
getAB                   Estimate beads-only shape parameters
getBF                   Calculate Bayes Factors
getExpected             Calculate expected read counts or proportion of
                        reads
guessEnriched           Identifying clearly enriched peptides
guessInits              Derive initial estimates of unknown model
                        parameters
runEdgeR                Run edgeR on PhIP-Seq data
summarizeRun            Summarize MCMC chain and return point estimates
                        for BEER parameters
summarizeRunOne         Derive point estimates for c, pi, phi, and Z
                        for a particular sample
